Problem Running Heudiconv

[tjhendrickson]

Summary

I am having difficulty converting my data to BIDS for a particular data set. In addition I am getting a strange error that I am not familiar with.

Here it is:

Traceback (most recent call last): File "/usr/local/bin/heudiconv", line 11, in sys.exit(main()) File "/usr/local/lib/python2.7/dist-packages/heudiconv/cli/run.py", line 125, in main process_args(args) File "/usr/local/lib/python2.7/dist-packages/heudiconv/cli/run.py", line 338, in process_args overwrite=args.overwrite,) File "/usr/local/lib/python2.7/dist-packages/heudiconv/convert.py", line 210, in prep_conversion getattr(heuristic, 'DEFAULT_FIELDS', {})) File "/usr/local/lib/python2.7/dist-packages/heudiconv/bids.py", line 72, in populate_bids_templates populate_aggregated_jsons(path) File "/usr/local/lib/python2.7/dist-packages/heudiconv/bids.py", line 150, in populate_aggregated_jsons save_json(task_file, fields, indent=2, sort_keys=True, pretty=True) File "/usr/local/lib/python2.7/dist-packages/heudiconv/utils.py", line 202, in save_json data, sort_keys=sort_keys, indent=indent) File "/usr/local/lib/python2.7/dist-packages/heudiconv/utils.py", line 231, in json_dumps_pretty "Values differed when they should have not. "
AssertionError: Values differed when they should have not. Report to the heudiconv developers

In addition I have gotten errors previously from the bids validator regarding the json field "TaskName" not existing.

Platform details:

Choose one:

• [ ] Local environment

• [X] Container

Custom singularity container. "singularity pull shub://tjhendrickson/BIDS_scripts"

• Heudiconv version:

0.5.2

[yarikoptic]

0.5.2

From the CHANGELOG for 0.5.3:

Fixed

• Do not shorten spaces in the dates while pretty printing .json

Could you please try 0.5.3 release and report back. If it is not fixed - you can rerun with --dbg flag, end up in pdb and discover which file is at fault -- or where strings differ (we should improve error message there though indeed). We should release 0.5.4 also very soon, but I do not think it carries any relevant to you changes.

[tjhendrickson]

Thanks for the suggestion. I tried upgrading heudiconv to 0.5.3 and got another error:

**Traceback (most recent call last): File "/usr/bin/heudiconv", line 11, in load_entry_point('heudiconv==0.5.3', 'console_scripts', 'heudiconv')() File "/usr/lib/python2.7/dist-packages/heudiconv/cli/run.py", line 125, in main process_args(args) File "/usr/lib/python2.7/dist-packages/heudiconv/cli/run.py", line 338, in process_args overwrite=args.overwrite,) File "/usr/lib/python2.7/dist-packages/heudiconv/convert.py", line 210, in prep_conversion getattr(heuristic, 'DEFAULT_FIELDS', {})) File "/usr/lib/python2.7/dist-packages/heudiconv/bids.py", line 72, in populate_bids_templates populate_aggregated_jsons(path) File "/usr/lib/python2.7/dist-packages/heudiconv/bids.py", line 140, in populate_aggregated_jsons j = load_json(task_file) File "/usr/lib/python2.7/dist-packages/heudiconv/utils.py", line 174, in load_json data = json.load(fp) File "/usr/lib/python2.7/json/init.py", line 291, in load kw) File "/usr/lib/python2.7/json/init.py", line 339, in loads return _default_decoder.decode(s) File "/usr/lib/python2.7/json/decoder.py", line 364, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/lib/python2.7/json/decoder.py", line 382, in raw_decode raise ValueError("No JSON object could be decoded") ValueError: No JSON object could be decoded

[mgxd]

hi @tjhendrickson - it looks like something was messed up when creating a task-<task>.json file - could you try deleting that file and reconverting?

What command are you calling to run heudiconv?